Lipid-Assisted Polymerization of Nucleotides

In addition to being one of the proponents of the “Lipid World hypothesis”, David Deamer, together with other colleagues, pioneered studies involving formation of RNA-like oligomers from their ‘non-activated’, prebiotically plausible monomeric moieties. In particular, the pioneering work in this regard was a publication from 2008 in Origins of Life and Evolution of Biospheres, The Journal of the International Astrobiology Society, wherein we described the formation of RNA-like oligomers from nucleoside 5’-monophosphates. In that study, we had simulated a terrestrial geothermal environment, a niche that is thought to have facilitated the prebiotic non-enzymatic synthesis of polynucleotides. We showed that a mixture of lipids and non-activated mononucleotides resulted in the formation of relatively long strands of RNA-like polymers when subjected to repeated cycles of dehydration and rehydration (DH-RH). Since 2008, terrestrial geothermal niches and DH-RH conditions have been explored in the context of several other prebiotic processes. In this article, we review the work that we and other researchers have carried out since then in this line of research, including the development of new apparatus to carry out the simulation of prebiotic terrestrial geothermal environments.

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Understanding Life: A Bioinformatics Perspective

European Review ◽

10.1017/s1062798716000570 ◽

2016 ◽

Vol 25 (2) ◽

pp. 231-245 ◽

Cited By ~ 4

Author(s):

Natalia Szostak ◽

Szymon Wasik ◽

Jacek Blazewicz

Keyword(s):

Origin Of Life ◽

Rna World ◽

Origins Of Life ◽

Life Itself ◽

Wet Lab ◽

The Origin Of Life ◽

To Come ◽

World Hypothesis ◽

Definition Of ◽

Rna World Hypothesis

According to some hypotheses, from a statistical perspective the origin of life seems to be a highly improbable event. Although there is no rigid definition of life itself, life as it is, is a fact. One of the most recognized hypotheses for the origins of life is the RNA world hypothesis. Laboratory experiments have been conducted to prove some assumptions of the RNA world hypothesis. However, despite some success in the ‘wet-lab’, we are still far from a complete explanation. Bioinformatics, supported by biomathematics, appears to provide the perfect tools to model and test various scenarios of the origins of life where wet-lab experiments cannot reflect the true complexity of the problem. Bioinformatics simulations of early pre-living systems may give us clues to the mechanisms of evolution. Whether or not this approach succeeds is still an open question. However, it seems likely that linking efforts and knowledge from the various fields of science into a holistic bioinformatics perspective offers the opportunity to come one step closer to a solution to the question of the origin of life, which is one of the greatest mysteries of humankind. This paper illustrates some recent advancements in this area and points out possible directions for further research.

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Prebiotic chemistry: a new modus operandi

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2011.0134 ◽

2011 ◽

Vol 366 (1580) ◽

pp. 2870-2877 ◽

Cited By ~ 72

Author(s):

Matthew W. Powner ◽

John D. Sutherland

Keyword(s):

Origin Of Life ◽

Early Life ◽

Rna World ◽

Origins Of Life ◽

Geochemical Conditions ◽

Systems Chemistry ◽

Novel Approach ◽

Sequential Addition ◽

World Hypothesis ◽

Emergence Of Life

A variety of macromolecules and small molecules—(oligo)nucleotides, proteins, lipids and metabolites—are collectively considered essential to early life. However, previous schemes for the origin of life—e.g. the ‘RNA world’ hypothesis—have tended to assume the initial emergence of life based on one such molecular class followed by the sequential addition of the others, rather than the emergence of life based on a mixture of all the classes of molecules. This view is in part due to the perceived implausibility of multi-component reaction chemistry producing such a mixture. The concept of systems chemistry challenges such preconceptions by suggesting the possibility of molecular synergism in complex mixtures. If a systems chemistry method to make mixtures of all the classes of molecules considered essential for early life were to be discovered, the significant conceptual difficulties associated with pure RNA, protein, lipid or metabolism ‘worlds’ would be alleviated. Knowledge of the geochemical conditions conducive to the chemical origins of life is crucial, but cannot be inferred from a planetary sciences approach alone. Instead, insights from the organic reactivity of analytically accessible chemical subsystems can inform the search for the relevant geochemical conditions. If the common set of conditions under which these subsystems work productively, and compatibly, matches plausible geochemistry, an origins of life scenario can be inferred. Using chemical clues from multiple subsystems in this way is akin to triangulation, and constitutes a novel approach to discover the circumstances surrounding the transition from chemistry to biology. Here, we exemplify this strategy by finding common conditions under which chemical subsystems generate nucleotides and lipids in a compatible and potentially synergistic way. The conditions hint at a post-meteoritic impact origin of life scenario.

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Colony-like Protocell Superstructures

10.1101/2021.09.16.460583 ◽

2021 ◽

Author(s):

Karolina Spustova ◽

Chinmay Katke ◽

Esteban Pedrueza Villalmanzo ◽

Ruslan Ryskulov ◽

C. Nadir Kaplan ◽

...

Keyword(s):

Mechanical Stability ◽

Critical Length ◽

Solid Surfaces ◽

Strand Displacement ◽

Shape Transformation ◽

Lipid World ◽

Membrane Envelope ◽

Membrane Bending ◽

World Hypothesis ◽

Aluminum Surfaces

AbstractWe report the formation, growth, and dynamics of model protocell superstructures on solid surfaces, resembling single cell colonies. These structures, consisting of several layers of lipidic compartments enveloped in a dome-shaped outer lipid bilayer, emerged as a result of spontaneous shape transformation of lipid agglomerates deposited on thin film aluminum surfaces. Collective protocell structures were observed to be mechanically more stable compared to isolated spherical compartments. We show that the model colonies encapsulate DNA and accommodate non-enzymatic, strand displacement DNA reactions. The membrane envelope is able to disassemble and expose individual daughter protocells, which can migrate and attach via nano-tethers to distant surface locations, while maintaining their encapsulated contents. Some colonies feature ‘exo-compartments’, which spontaneously extend out of the enveloping bilayer, internalize DNA, and merge again with the superstructure. A continuum elastohydrodynamic theory that we developed reveals that the subcompartment formation must be governed by attractive van der Waals (vdW) interactions between the membrane and surface. The balance between membrane bending and vdW interactions yields a critical length scale of 273 nm, above which the membrane invaginations can form subcompartments. The findings support our hypotheses that in extension of the ‘lipid world hypothesis’, protocells may have existed in the form of colonies, potentially benefiting from the increased mechanical stability provided by a superstructure.

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Possible Roles of Amphiphilic Molecules in the Origin of Biological Homochirality

Symmetry ◽

10.3390/sym11080966 ◽

2019 ◽

Vol 11 (8) ◽

pp. 966 ◽

Cited By ~ 1

Author(s):

Nozomu Suzuki ◽

Yutaka Itabashi

Keyword(s):

Physical Properties ◽

Origin Of Life ◽

Supramolecular Assembly ◽

Spontaneous Formation ◽

Amphiphilic Molecules ◽

Lipid World ◽

The Origin Of Life ◽

Compositional Information ◽

World Hypothesis ◽

Biological Homochirality

A review. The question of homochirality is an intriguing problem in the field of chemistry, and is deeply related to the origin of life. Though amphiphiles and their supramolecular assembly have attracted less attention compared to biomacromolecules such as RNA and proteins, the lipid world hypothesis sheds new light on the origin of life. This review describes how amphiphilic molecules are possibly involved in the scenario of homochirality. Some prebiotic conditions relevant to amphiphilic molecules will also be described. It could be said that the chiral properties of amphiphilic molecules have various interesting features such as compositional information, spontaneous formation, the ability to exchange components, fission and fusion, adsorption, and permeation. This review aims to clarify the roles of amphiphiles regarding homochirality, and to determine what kinds of physical properties of amphiphilic molecules could have played a role in the scenario of homochirality.

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Spontaneous formation of prebiotic compartment colonies on Hadean Earth and pre-Noachian Mars

10.1101/2021.05.11.443509 ◽

2021 ◽

Author(s):

Elif Senem Koksal ◽

Inga Poldsalu ◽

Henrik Friis ◽

Stephen Mojzsis ◽

Martin Bizarro ◽

...

Keyword(s):

Aqueous Media ◽

Physical Interaction ◽

Shape Transformation ◽

Naturally Occurring ◽

Dna Strand Displacement ◽

Lipid World ◽

Displacement Reactions ◽

Freely Suspended ◽

Dna Strand ◽

World Hypothesis

The primitive cells that emerged at the origin of life are commonly viewed as spherical biosurfactant shells, freely suspended in aqueous media (1-3). This model explains initial, but not subsequent events in the development process towards structured protocells. Taking into consideration the involvement of naturally occurring surfaces, which were abundant on the early Earth (4), we report feasible and productive pathways for the development of primitive cells. Surfaces intrinsically possess energy, easily utilized by the interfacing amphiphiles, such as lipids, to attain self-organization and spontaneous transformations (5-7). We show that the physical interaction of phospholipid pools with 20 Hadean Earth analogue materials as well as a Martian meteorite composed of fused regolith representing the ancient crust of Mars, consistently lead to the shape transformation and autonomous formation of surfactant compartment assemblies. Dense, colony-like protocell populations grow from these lipid deposits, predominantly at the grain boundaries or cleavages of the investigated natural surfaces, and remain there for several days. The model protocells in our study are able to autonomously develop, transform and pseudo-divide, and encapsulate RNA as well as DNA. We also demonstrate that they can accommodate non-enzymatic, DNA strand displacement reactions. Our findings suggest a feasible route towards the transformation from non-living to living entities, and provide fresh support for the 'Lipid World' hypothesis (8).

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